Spatially resolved single-cell analysis of transcriptomic changes linked with neuropathic pain in human neuromas

Injuries to the trigeminal nerve, responsible for sensory innervation to the face, may occur during routine dental procedures, resulting in the formation of a neuroma accompanied by loss of sensation and/or symptoms of pain. To gain insight into the molecular mechanisms underpinning the sensory changes, single nuclei RNA sequencing and spatial transcriptomics were used to profile the transcriptional landscape at single cell resolution of human trigeminal nerves and neuromas. Cellular and transcriptional changes were identified that correlated with the presence of pain, including an expansion of endothelial cells with a proinflammatory phenotype and overexpression of HLA-A, CXCL2, and CXCL8. Interactome analysis highlighted signaling changes linked with the presence of pain. HLA-A protein expression was confirmed in neuromas and positively correlated with symptoms of pain. Our data provide a detailed spatial overview of the cell types that populate human peripheral trigeminal nerves, in health and injury, and their transcriptional profile. The comparison of painful and nonpainful samples highlights several changes in cellular composition, transcriptome and inferred molecular signaling linked specifically with the presence of pain, and also a novel role for HLA-A in neuropathic pain. Our findings represent a valuable resource for pain research, highlighting the role of inflammation, endothelial cell dysfunction, and chemokine signaling in neuropathic pain.